PAGE5

PAGE family member 5, the group of PAGE family

Basic information

Region (hg38): X:55220345-55224108

Links

ENSG00000158639 ∙ NCBI:90737 ∙ OMIM:301009 ∙ HGNC:29992 ∙ Uniprot:Q96GU1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PAGE5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAGE5 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in PAGE5

This is a list of pathogenic ClinVar variants found in the PAGE5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-55220607-C-T		not specified	Uncertain significance (Mar 29, 2023)
X-55221387-G-A		not specified	Uncertain significance (Mar 07, 2024)
X-55221449-G-A		not specified	Uncertain significance (Apr 30, 2024)
X-55221453-G-A		not specified	Uncertain significance (Oct 16, 2023)
X-55221788-A-G		not specified	Uncertain significance (Mar 27, 2023)
X-55221792-G-T		not specified	Uncertain significance (Nov 14, 2023)
X-55221798-A-G		not specified	Uncertain significance (Aug 01, 2023)
X-55221842-G-C		not specified	Uncertain significance (Jun 16, 2024)
X-55221869-G-A		not specified	Uncertain significance (Jan 30, 2024)
X-55222675-C-A		not specified	Likely benign (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAGE5	protein_coding	protein_coding	ENST00000289619	5	3754

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0207	0.764	125709	1	5	125715	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.387	38	45.3	0.838	0.00000318	828
Missense in Polyphen		5	9.5781	0.52202		213
Synonymous	-0.586	19	16.0	1.19	0.00000113	250
Loss of Function	0.871	3	5.13	0.585	3.25e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000146	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000435	0.0000264
Middle Eastern	0.000146	0.000109
South Asian	0.0000575	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.593
• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.79

Haploinsufficiency Scores

• pHI: 0.0984
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0102

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Molecular function: protein binding